The problem with killing Sasuke was he had been the last remaining Uchiha member, since Itachi's remains lay moldering in some half-forgotten place and the rest of the clan had been slaughtered years before. This, Sasuke being the last Uchiha, had been a concern, and had been the main argument for why he should he be kept alive. With Sasuke dead, the Uchiha clan would be erased from the world, and with the loss of the Uchiha clan would come the loss of the Sharingan. Not that losing the Uchiha clan was that terribly tragic, after all, hundreds of clans all over the world were destroyed everyday. That is not to say that people were not upset by the loss of the Uchiha, but the death of a clan was something that people could deal with. No, people were more worried about losing the Sharingan, for only Uchiha could learn the Sharingan. Of course, each clan that was lost also had some magical kekkei genkei, but losing the Sharingan seemed worst for some reason. More personal.
But there was little that could be done. Itachi was dead, Sasuke was dead, and if there were any surviving clan members out there, they were doing a good job of keeping themselves hidden. So people lamented the loss of the Sharingan, and they wept for Sasuke, though secretly, many were happy to see him dead. It was said that Itachi had been the crazy one; people who said that had clearly never met Sasuke. So they cried, and wept and shook their fists at the sky. But after a while, they started getting back to their normal lives. There were children to raise, and shinobi to train, not to mention the fact that Konoha had to be rebuilt. So while they mourned the last of the Uchiha, after a while, the people of the Hidden Leaf forgot and moved on with their lives.
At first, they completely forgot about Kakashi Hatake.
Of course, why should they remember Kakashi? He, after all, was not an Uchiha by birth. And his knowledge of the Sharingan was scant; Itachi and Sasuke had taken the best secrets of the Uchiha Clan kekkei genkei to the grave. But little was better than nothing, so it on Kakashi that all the tattered and broken plans made for Sharingan wielders lay. Or were lay, once people remembered that the Sharingan wasn't completely gone.
But this, in turn, brought up another issue. When an Sharingan wielder from the Uchiha clan died, that had been no big deal. After all, why should it be a big deal. True, death was sad, and whomever it was would undoubtedly be mourned, but there would always be other clan members to 'take up the mantle'. With the Uchiha clan gone, this was no longer true. Once Kakashi died, that would be it. There wouldn't be any loopholes, or short-cuts. When Kakashi died, that would be the end. And this time, the end would be forever.
The solution to this problem was so obvious that when they realized the solution, it was literally painful to realize it had taken them this long to figure the solution out. If not for Rin and Obito, Kakashi would have never become a Sharingan user. He would have gone through life as a perfect shinobi, strong, ruthless, and one who obeyed the rules without question. True, Kakashi would have been a good ninja without the Sharingan. But he would have been an ordinary one.
The answer to all their problems was just so simple, so complex, so...perfect.
There was always one student at the Academy who is better than the rest. Stronger, smarter, just better. Sometimes that person is a boy. Sometimes that person is a girl. It does not really matter. Either way, you still end up with a student who is just a little bit better than the rest.
So their plan, their brilliant plan, went like this; take that student, that one student who was better than the rest, and train them. Make them stronger and smarter than anyone else. Make them the best shinobi they can possibly be trained to be. Or if they are a girl, the best kunoichi they can possibly be trained to be. Pull them out of the Academy, and have them be trained one-on-one. And then, when the teachers deems they are ready, operate. Take out one of their bland, ordinary eyes, and replace that eye with a jewel, a treasure among treasures; the last surviving Sharingan eye. Obito's eye. Kakashi's eye. If their plan worked, said eye would be passed down generation through generation, going only from the best to the best.
Their plan was not perfect, nor was it moral. Their plan had flaws and faults. But all things considered, their plan was the best that could be come up with. Their world was a cruel world, and they had to make the best of a ruthless fate.
Once upon a time, a wise man once said "An eye for an eye makes the whole world blind." And that was true. But their world was a cruel world, a ruthless world, and a blinded world. A world in which right and wrong are often the same thing. A world in which many choices end with death, either yours, or someone else's. A world in which children are trained to be killers, and no one complains.
An eye for an eye will make the whole world blind.
But as Itachi Uchiha proved, even the blind could see with the Sharingan. Your normal eye-sight might fail, but with the Sharingan, you would still see.
Their plan was a flawed plan. But it was all they could come up with. So then...
An eye for an eye.